Microbiome is the fancy new name for what is commonly called gut bacteria and other bacteria systems that keeps us alive. Without the microbiome we would die. All microbiomes are not the same — in fact, the microbiome you have is connected strongly with your DNA and is actually more unique than your DNA. A recent study of  identical twins found that they can be told apart by their microbiome and not by their DNA.

You have around 100 trillion bacteria according to a recent New York Times article which states:

Our resident microbes also appear to play a critical role in training and modulating our immune system, helping it to accurately distinguish between friend and foe and not go nuts on, well, nuts and all sorts of other potential allergens. Some researchers believe that the alarming increase in autoimmune diseases in the West may owe to a disruption in the ancient relationship between our bodies and their “old friends” — the microbial symbionts with whom we coevolved.

The article goes on and describes higher rates of allergy, asthma and autoimmune problems when a mother’s microbiome is not transfered to a child because of a C-section. The mother’s microbiome appears to be DNA compatible with the child. Microbiomes from another person may be rejected or fail to thrive.

A 2009 article provides some interesting insights:

• Members of the genera Bacteroides, Eubacterium, Clostridium and Ruminococcus were the major species found in the adult microbiota. – Lactobacillus species which makes up most probiotics are actually a minor player.
•  For instance, E. coli K12 had a ratio of 3.4% for adult gut-enriched genes, – there are other E.Coli present.

Bacteria also produces their own virus to kill other bacteria as reported in this 2012 article. Often one species of a family will try to kill off other species of the same family. Counting the volume of a family of bacteria does not determine if they are good ones or bad ones. There are good E.Coli and there are bad E.Coli. The same applies to Lactobacillus — Lactobacillus endocarditis is a known killer. The belief that Lactobacillus is the dominant bacteria in the gut is dogma as a recent paper states. This same paper states “It is important to note that the majority of traditional probiotic strains are probably allochthonous to the intestinal tract, and they show very little ability to persist in the human gut.”

What does Microbiome impact?

The simple answer is…. EVERYTHING.  A few sample studies:

• inflammatory gastrointestinal disease
• cognition
• changes in gut microbiota are related to obesity (thus inability to gain or loose weight)
• B12 levels (Lactobacillus Reuteri produces most of it)
• cancer

Your Microbiome is unique to you — thus you CFS/FM may also be unique to you!

If my best hypothesis on what causes CFS/FM is correct (a stable dysfunction of your microbiome) then every patient will have a different dysfunctional variations of their microbiome! The reality of medical tests is that at best only a small percentage of the species can be determined by the best academic test procedures (not available at commercial labs) using PCR and DNA fragments. Many species cannot be kept alive outside of the body which makes study difficult.

On the plus side, it appears very possible to disrupt this stable dysfunction — effectively declaring war against it by both killing off the offending population and then aggressively repopulating it with good ones! The disruption is not easy — before the arrival of antibiotics, one disease that was associated with a stable dysfunction was successfully treated by inducing a feeble infection – often cholera. It turns out that many infections changes the microbiome which usually returns to normal after the infection. In some cases, this fails to happen and the microbiome remains in a changed state (the percentage for one group of diseases appears to be 4-8%). The “flu like illness” often reported before CFS may actually be flu or some other illness. The CFS may results from the microbiome not returning to normal.

There is some art in this process of disrupting this dysfunctional microbiome that needs to based on hard science. In following posts, I will share my current understanding and experience in being an anarchist against this dysfunctional microbiome. The key items are:

• Killing off bad species (may have collateral damage on the good species) – antibiotics, herbs, spices
• Feeding the good species (so they start to dominate) – prebiotics, often FOS, but there are other things
• Importing good species (a.k.a. probiotics of the appropriate type, fermented foods, raw milk and fecal transplants)
• Starving the bad species (so there are less of them) – no gluten and no sugar diets are likely doing this